Genetics of Chronic Mountain Sickness in Andean Highlanders Nov. 2, 2013 Roy Ronen University of California, San Diego

2 Acute Mountain Sickness headaches fatigue, weakness dizziness insomnia … Chronic Mountain Sickness Polycythemia Palpitations Tinnitus >> pulmonary hypertension >> stroke >> poor birth outcome … Me, circa 2006 Years Days Salt plains (Salar de Uyuni), Bolivia, 3800m

a ‘recent’ example Andean Mountains, Peru Himalaya Mountains, Tibet Bale Mountains, Ethiopia 58% sea level O 2 61% sea level O 2 56% sea level O 2 Positive Darwinian Selection 3 -Scheinfeldt et al Alkorta-Aranburu et al Huerta-Sanchez et al Beall et al Bigham et al Simonson et al Yi et al. 2010

High Altitude Adaptation migration to high altitude High alt. population Andean Mountains, Peru 58% see level O 2 Time Now

Low alt. population Time MRCA Out-group population migration to high altitude High alt. population High Altitude Adaptation Now

WGS (~30x) of 10 CMS, 10 non-CMS Setup ADMIXTURE, k=4 Control: 66 MXL (Mexican, LA) 1000G, low pass WGS Outgroup: 67 LWK (Luhya, Kenya) 1000G, low pass WGS

Setup ‘all’ sites (approx. freq.) few sites (accurate freq.) Selection Scan WGS Arrays -Scheinfeldt et al Alkorta-Aranburu et al Huerta-Sanchez et al Beall et al Bigham et al Simonson et al Yi et al. 2010

8 Whole Genome Sequencing Chromosome 19, S π SNP Frequency Profile (chr19) Genotyping Array (Affy 6.0) SNP Frequency Profile (chr19) Chromosome 19, S π

Low alt. population Time MRCA Out-group population migration to high altitude High alt. population Genome Wide Scan for Selection S π, S f, F ST, PBS

10 Chr12, q13.11

SENP1 – Regulates GATA1 and HIF1 α (!!!) – Senp -/- mice show erythropoiesis defect PFKM – pfkm deficient mice show hyper vascularization, muscle hypoxia, and exercise intolerance ANP32D – Oncogene… Known Functions

Measure Expression Experimental Results (1) Normoxia controls Fibroblast cell lines derived from CMS & nonCMS Hypoxia 1.5% O 2

Experimental Results (2) RNAi knock down of Drosophila orthologs Normal (21 % O 2 ) Hypoxia (5 % O 2 ) % Survival SENP1 ortholog ANP32D ortholog Condition

Summary 1.WGS important for identifying signature of selection. 2.New (experimentally validated!) hypoxia-tolerance genes: Selection of ANP32D, SENP1 in non-CMS (vs. CMS/MXL). Transcripts highly expressed in CMS vs. non-CMS. Knock downs remarkably more tolerant to hypoxia. 14 Whole Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders American Journal of Human Genetics, Sept. 2013

UC San Diego Vineet Bafna Lab Vineet Bafna Lab – Nitin Udpa Gabriel Haddad Lab Gabriel Haddad Lab – Dan Zhou – Tsering Stobdan – Huiwen Zhao Acknowledgments BGI Junbin Liang Yingrui Li Yi Yin Yuanping Du Lixia Guo Rui Cao Yu Wang New Mexico HEMC Otto Appenzeller Universidad Peruana Cayetano Heredia Francisco Villafuerte David Callacondo Xin Jin Chen Huang Wenlong Jia Dandan Cao Guangwu Guo Siqi Liu Vanderbilt Med. Center Jorge L. Gamboa